Our long-term objective is to develop methods to prevent and treat coccidioidomycosis, a systemic fungal disease of otherwise healthy humans caused by the fungi Coccidioides immitis and Coccidioides posadasii. The collaborating investigators are John Taylor and Garry Cole, directors of laboratories that study Coccidioides molecular developmental and evolutionary biology, respectively. Our goal in this proposal is to focus the tools of comparative genomics and gene expression on Coccidioides to identify genes important to pathogenicity and virulence. Two of our findings underlie our proposal: 1) disruption of genes known to be important to the pathogenicity of Coccidioides reduces its virulence in mammals, and 2) Coccidioides shows genetic variation among five geographic populations. The availability of complete, annotated genomes of each /coccidioides species and the genome of their non-pathogenic relative, Uncinocarpus reesii, is a major pillar of support for our project. We can greatly increase the number of targets for therapy or prevention by searching the genome for pathogenicity genes, while accounting for natural variation. We will evaluate our hypotheses about these genes by virulence tests in mice. Our specific aims are to: identify genes unique to Coccidioides as compared to Uncinocarpus, identify genes that show positive selection between Coccidioides species and compared to Uncinocarpus, and identify genes in Coccidioides with significant transcription differences between the saprobic and parasitic phases, both in vitro and in vivo. From this cadre of unique genes which are under positive selection and upregulated during the parasitic phase, we will identify a pool of putative pathogenicity genes that can we will test by assessing virulence in mice of the wild-type strain, the WT strain in which the gene of interest has been knocked out, and the KO strain with the gene of interest replaced. Via existing collaboration, our laboratories have studied and published on natural selection of Coccidioides pathogenicity genes and assessed transcription in the saprobic and parasitic phases. Relevance to public health: Nearly 10% of Americans live in areas endemic to coccidioidomycosis, and approximately 5% of those infected develop life-threatening disease. Symptomatic infections confer long term immunity, so vaccination is possible. Likewise, virulence is reduced when pathogenicity genes are disabled, which indicates that pharmaceutical targeting of these gene products should be efficacious.